SOMERVILLE — Pity the Mystic.
The gritty 7-mile river that flows from Medford and Arlington to Boston Harbor rarely earns better than a “D” on the federal government’s annual water quality report card. Raw sewage still spews into the river during severe storms — including almost 4 million gallons in December. Vast mats of invasive water chestnut clog the surface in places.
Almost 30 years after Boston’s sewage-laden shores began their transformation into sparkling, swimmable beaches, the Mystic — one of the three main rivers that flow into the harbor — lags far behind the beloved Charles or scenic Neponset in water quality and public access. Hidden in spots and surrounded by asphalt, it serves as a stark symbol of the cleanup challenges remaining for waterways in cities nationwide.
“When you go downstream, really, it’s an urban ditch,’’ said Neil Clark, who lives on one of the two Mystic Lakes that drain into the river and knows the area well. “It is just down-beaten.”
The Mystic — the namesake of the celebrated Dennis Lehane crime novel — has long suffered in the shadow of the longer and more visible Charles and Neponset rivers. It is a far cry from the idyllic waterway portrayed in the popular Thanksgiving poem “Over the River and Through the Woods,” with densely settled suburban towns such as Medford in its northern reaches and scrap metal plants and tank farms downstream in Everett and Chelsea.
But it is starting to attract attention, as more development is proposed near the river, including casino magnate Steve Wynn’s bid to build a casino and resort on the site of a former Monsanto Chemical plant in Everett. A herring run was robust last year, and the Environmental Protection Agency has stepped up enforcement to prevent illegal discharges of pollutants into the Mystic, including fining Suffolk Downs $1.25 million last year for dumping horse manure and urine into a nearby wetland.
Court-ordered work to separate sewer pipes from storm drains is underway in Cambridge and Somerville, including a $116 million project for Alewife Brook, which flows into the Mystic. And the environmental advocacy group Conservation Law Foundation, hoping to accelerate the pace of the Mystic cleanup, began suing scrap metal plants near the river last year,saying they did not have proper permits to discharge industrial pollutants.
Yet ever since the EPA began grading the Mystic seven years ago, there has been no lasting improvement in water quality, largely because the river faces so many of the persistent problems of urban rivers: Sewer and storm pipes overflow, and pet waste, industrial pollutants, and lawn fertilizer drain from acres of surrounding paved surfaces. While the Charles and Neponset have some of the same challenges, the Mystic’s are more extensive, many water specialists agree.
“You name the problem, we have it,’’ said EkOngKar Singh Khalsa, executive director of the Mystic River Watershed Association. “Part of the problem is that we were settled first, we are so old. People perceive this river as ruined, but it is a living system that is struggling to thrive.”
Khalsa and other advocates say severe cuts to the state Department of Environmental Protection’s budget have stymied progress, as has the agency’s reluctance to fine communities for not stopping pollution such as leaking sewage.
Kenneth Kimmell, DEP commissioner, said the agency has worked hard, despite deep budget constraints, to take aggressive action to clean up the river. Cuts forced his agency to halt a two-year effort in 2009 to track pollution in the river to its source, but that may soon change if the Legislature approves money for the testing.
“A clean and healthy Mystic River is a high priority,” said Kimmell. “The governor’s proposed budget would enable us to reinstate that program and get the river cleaned up more quickly and more thoroughly.”
Advocates for the river also decry periodic large dumps of raw sewage. During a stormy Dec. 27, Massachusetts Water Resources Authority workers released a mix of untreated sewage and rainwater into the river across from the Medford Whole Foods Market to relieve pressure on the system. In all, almost 4 million gallons of the sludge flowed into the river from various discharge pipes.
River advocates are concerned that the volume of releases into the Mystic might far exceed those into the Charles and Neponset, but they say they do not know for sure because reporting has not always been accurate.
“Although these releases are well-known and well-understood, they are in fact violations of the Clean Water Act,’’ said Khalsa.
Massachusetts Water Resources Authority officials say they are working hard to stop such releases, but they come only about once a year and tend to flush out of the system quickly. And if they did not occur, they add, the entire system would back up during heavy storms. They say their data — based on water quality readings from the middle of the Mystic, as opposed to testing near tributaries as the watershed association does — show the river’s water quality is on par with the Charles.
“We view these [releases] as something of a last resort, but the lesser of two evils,’’ said Fred Laskey, the water agency’s executive director.
Those large releases are only a piece of the problem. A bigger one may be pavement: It is difficult to prevent waste from washing into a river from every street, parking lot, and sidewalk. The Mystic flows through communities with an enormous amount of pavement — 77 percent of Somerville’s land area is paved over, for example — that prevents rainwater from seeping into the ground to be cleansed.
“In many ways, these are the next-generation environmental challenges,’’ said Bruce Berman of Save the Harbor/Save the Bay, a Boston-based advocacy group. Fixing those problems requires a reengineering of cities to keep water local, such as using barrels to catch rainwater flowing off roofs to water plants, or developing porous pavement to let rain seep into the earth.
Yet Berman and other river advocates say there is an easier way to help the Mystic: Make it more visible, as a way to build public, and then political, support to clean it.
Unlike the Charles that flows through the heart of Boston and the Neponset, which is garnering attention in part from a new bike trail along its most densely populated areas, the Mystic is largely hidden behind fences, industrial sites, and old buildings.
Many of the communities along its filthiest parts are poor. The watershed association holds yearly kayak and canoe races and cleanups, but making the Mystic more accessible remains a challenge.
There is no better time to get the public involved, advocates say, because the Mystic may be in for worse news. The EPA announced last month that it is working on new language to give financially struggling communities more time to comply with Clean Water Act regulations. Requests to the EPA for comment went unanswered.
“The real message there . . . is we are going to make it easier for you to pollute,’’ said Christopher Kilian, director of the Conservation Law Foundation’s Clean Water Program. “We made a decision as a society that these public resources were going to be treated the same . . . all waters were going to be protected equally. I worry about the Mystic.”